title: Bh_ML

description:
Fully expanded mature leaves of 6-month-old Boea hygrometrica.
processed data file: Differentially methylated region.xlsx

source_name: mature leaves

extract_protocol:
For each of the two samples (Bh_ML and Bh_YL), five biological replicates, each containing 30 leaf discs, were mixed for genomic DNA (gDNA) isolation. gDNA was extracted using a Plant Genomic DNA Extraction Kit (BioTeke) and then qualified using a Qubit Fluorometer (Invitrogen).
Five micrograms of purified genomic DNA was sonicated and ligated to Illumina methylated DNA adapters (San Diego, CA), after which adapter ligated molecules of 120–170 bp were enriched by 18 cycles of PCR with primers complementary to the adaptor sequences.

treatment_protocol: Young and mature leaf samples were collected from 1- and 6-month-old sterile parent plants, respectively.

value: mature leaves

tag: developmental stage

value: untreated


title: Psojae_WT_MY_H3K27me3_rep1

status: Public on Nov 25 2019

type: SRA

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

country: China

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
Clean reads were aligned to Psojae v1.1 and Pinfestans whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Genome_build: Psojae v1.1
Supplementary_files_format_and_content: Bigwig files, scores represent enriched value(log2(fold-change))

molecule: genomic DNA

organism: Phytophthora sojae

source_name: mycelium

growth_protocol: V8 medium

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

tag: strain

tag: tissue

value: mycelium

tag: chip antibody


title: mac3a mac3b mRNAseq rep2

city: Beijing

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

library_source: transcriptomic

data_processing:
All sequenced reads were collapsed to non-redudant reads and mapped back to Araport 11 genome using STAR with maximum 8 mismatches.
Genome_build: Araport 11
Supplementary_files_format_and_content: Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: unopened flower buds

growth_protocol: Plants were grown with 16hr of light at 22 °C

extract_protocol:
The total RNA was extracted with trizol, and treated with Dnase I to clean up the genomic DNA contamination
All the libraries were built using directional RNA libraries preparation kit s(NEB) using different RNA input including rRNA-depleted  tota RNA,  rRNA-depleted  chromatin RNA, mRNA

tag: genotype/variation

value: mac3a mac3b

tag: molecule

value: rRNA-depleted Total RNA


title: naked mole-rat circulating immune cells saline control sample 1 replicate 2

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

state: CA

address: 1170 Veterans blvd

country: USA

institute: Calico

data_processing:
Single-cell fastq files were demultiplexed to their respective barcodes using the 10X Genomics Cell Ranger mkfastq utility
Unique Molecular Identifier (UMI) counts were generated for each barcode using the Cell Ranger count utility using the mm10 reference genome and the mouse Gencode version M12 annotation  for mouse and HetGla2.0 reference genome along with the RefSeq GCF_000247695.1 annotation for naked mole-rat
For each single-cell sample barcodes that were not likely to represent captured cells were filtered out by detecting the first local minimum above 2 in a distribution of log10(#UMIs).
For each single-cell sample genes that are too sparsely captured across barcodes were filtered out by detecting the first local minimum above 3 in a distribution of log10(#barcodes)
For each single-cell sample barcodes capturing more than a single cell (multiplets) were sought as local modes in the distributions of log10(#genes) and log10(#UMIs), whose x-axis maxima are more than 1.5 higher than that of the x-axis location of the global maximum of the respective distribution and includes less than 5% of the total number of barcodes
Whole spleen RNA read data were mapped using STAR aligner version 2.5.3a
Transcript and gene abundances of whole spleen mapped RNA read data were quantified using MMSEQ
Genome_build: For mouse: mm10 reference genome and the mouse Gencode version M12 annotation. For naked mole-rat the HetGla2.0 reference genome and the RefSeq GCF_000247695.1 annotation for naked mole-rat
Supplementary_files_format_and_content: For the single-cell data processed data files are comma separated matrices of UMI counts where rows are gene IDs (Ensembl for mouse and Entrez for naked mole-rat) and columns are barcodes. The genes and barcode that are included are those that were retained following all filtering steps

organism: Heterocephalus glaber

source_name: single circulating immune cells

extract_protocol:
10X Genomics Chromium Controller droplet emulsion capture
10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing
Single cells were extracted using 10X Genomics Chromium Controller droplet emulsion capture. Whole tissue RNA was purified using 1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Single cell libraries were contructed using 10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing. Whole spleen RNA libraries were contructed using Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit

treatment_protocol: all animals were anasthesiasized with isoflurane. Saline controls received an intraperitoneal 200µl sterile saline injection. LPS-chllaneged animals received an intraperitoneal 1mg/kg lipopolysaccharide injection

value: single circulating immune cells

tag: condition

value: saline control

tag: Sex

value: male

tag: age

value: 23-25 months old


title: SO3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
After importing of FASTQ files, raw sequencing reads were trimmed based on quality score (Q-score >20 was considered high-quality data), removal of adaptor sequences and discarding reads with length <15 bp.
Sequence reads were mapped and annotated to the Sus scrofa reference genome with genes and transcripts
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization)
Expression analysis has been done using Differential Expression In Two Groups tool of CLC Genomics Workbench v. 12.0 based on a negative binomial Generalized Linear Model (GLM) function.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: A matrix table including total read count and Tags Per Million (TPM) values for each sample with gene ID.

organism: Sus scrofa

source_name: Oocyte

extract_protocol:
Total RNA was isolated from denuded oocytes of the two different groups (three replicates each, n= 360) using an AllPrep DNA/RNA Micro Kit (Qiagen) according to the manufacturer’s instructions.
The RNA libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Porcine ovaries were collected from prepubertal gilts at a local abattoir and transported to our laboratory in flask within 3 h after slaughter. Ovaries were washed three times with saline solution. COCs were aspirated from small follicles with diameter 1.5-1.9 mm (SO) using a 23-gauge needle attached to a 5 mL syringe or from large follicles with diameter from 3 to 6 mm (LO) using 20-gauge needle attached to a 10 mL syringe.

value: Prepubertal gilts

tag: size


title: mac3a mac3b mRNAseq rep1


title: naked mole-rat circulating immune cells saline control sample 1 replicate 1


title: Ecoli_rne(ΔMTS)_T2_kinetic2

type: RNA

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

description:
Escherichia coli MG1672
Cells were in mid-exponential phase, the sampling was performed 2 minutes after rifampicin addition. It is the second kinetics out of 3 for this strain.

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing:
Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used. Only a normalization between arrays according to an invariant probeset intensities was performed. For each strain, a set of probes in the background for which the ranks were roughly invariant across all twelve arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.
After normalization, in each array, transcript-specific intensity was computed as the median value of the 16 targeting probe intensities.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli, rne(ΔMTS), Sampling 2 minutes after rifampicin addition in kinetic 2

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit.

growth_protocol: The laboratory strain E. coli K12 MG1655 referred as the rne+ strain and its mutant strain E. coli rne (ΔMTS) were grown in bioreactors in M9 glucose (3g/l) at 37 °C. The pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Each culture was repeated three times to provide independent biological kinetics.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively.

treatment_protocol: In mid-exponential phase, samples were collected for the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit the initiation of transcription, and cells were harvested at three different time points after this addition. Cultures were performed in triplicate. Samples were immediately frozen in liquid nitrogen upon collection.

value: rne(deltaMTS)

tag: treatment

value: rifampicin

tag: sampling time

value: 2 minutes after rifampicin addition

tag: repetition

value: kinetic 2


title: Ecoli_rne(ΔMTS)_T1_kinetic1

description:
Escherichia coli MG1668
Cells were in mid-exponential phase, the sampling was performed 1 minute after rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 1 minute after rifampicin addition in kinetic 1

value: 1 minute after rifampicin addition

value: kinetic 1


title: Pyruvate at 6 hours, Replicate 2

city: London

first: Luiz

middle: Pedro

last: de Carvalho

address: 1 Midland Road

department: Laboratory of Mycobacterial Metabolism and Antibiotic Research

country: United Kingdom

institute: The Francis Crick

description: Ribosomal depleted total RNA

data_processing:
Alignment: bowtie2: Version 2.1.0
Sam to Bam Conversion: samtools view : Version 1.2
Raw Coverage Extraction: samtools bedcov: Version 1.2
Normalisation: DESeqDataSetFromMatrix( raw.counts, design ~ time.point + condition + time.point:condition); :DESeq2 package for R-3.3.1
Normalised data export: estimateSizeFactors(); counts(, normalised = TRUE);DESeq2 package for R-3.3.1
Differential Expression Calling: DESeq()
Genome_build: Mtb_H37Rv
Supplementary_files_format_and_content: Transcriptome_of_MTB_H37Rv_raw_feature_counts.txt: tab delimited text file of un-normalised read counts per-feature

organism: Mycobacterium tuberculosis

source_name: Bacteria

growth_protocol: H37Rv was grown in 100ml of complete 7H9 supplemented with 0.5% bovine serum albumin 0.2% dextrose, 0.85% NaCl, 0.05% tyloxapol and 0.2% glycerol in roller bottles. When the culture reached a OD600=0.5-0.6, the cells were harvested and washed three times with 7H9 without supplement. Then, they were suspended in 100ml of fresh 7H9 supplemented with the specific carbon source (selected between D-glucose, L-lactate, pyruvate) at the final concentration of 0.4%. The samples were collected after 6hr and 24h

extract_protocol:
The cells were harvested by centrifugation 3,000g at 4°C for 5 min, supernatant was removed and the pellet frozen until the extraction.Total RNA was extracted according to the FastRNA Pro Blue kit manual (MP). The cells were ribolyzed three times (40s /6.0), incubating in ice for 1 minute between pulses. To remove genomic DNA the samples were treated twice with TurboDNase (Ambion) for 1hr at 37°C. Total RNA was purified and concentrated to 20µl of DEPC water using RNA clean-up kit (Zymoresearch) and quantified by Qubit. 2.5ng of RNA were used to check the removal of DNA by PCR . The nucleic acid integrity was verified by Bioanalyzer (Agilent RNA 6000 Nano). RNAs were extracted by FAST Blue kit (MPBio) and suspended in a final volume of 100 ul. The concentration was evaluated by spectrophotometer (Nanodrop, ND-1000) and integrity by RNA6000 Nano reagents and Agilent 2100 Bioanalyzer. 5µg or each RNA samples were depleted of rRNA using the Ribo-Zero Magnetic Kit (Epicentre). The samples were purified using Qiagen RNeasy MinElute Cleanup Kit by means of modified protocol suggested in the Ribo-Zero Magnetic Kit to allow recovering small RNAs. RNA was quantified by Qubit.
Libraries were prepared by ScriptSeq v2 (Epicentre cat. SSV21124), FailSafe Enzyme Mix Only (Epicentre) and Index PCR primers (Epicentre, Cat. No. RSBC10948). The libraries was sequenced with an Illumina Hi-Seq 4000 instrument.

value: Pyruvate at 6 hours


title: Pyruvate at 6 hours, Replicate 1

description: Ribosomal depleted total RNA


title: naked mole-rat circulating immune cells sample 3

value: normal

value: female


title: naked mole-rat spleen saline control sample 2 replicate 2

source_name: single spleen cells

value: single spleen cells


title: naked mole-rat circulating immune cells sample 4


title: naked mole-rat spleen LPS-challenged sample 1 replicate 2

value: LPS challenge


title: Pyruvate at 24 hours, Replicate 3

description: Ribosomal depleted total RNA

value: Pyruvate at 24 hours


title: Ecoli_rne(ΔMTS)_T9_kinetic1

description:
Escherichia coli MG1670
Cells were in mid-exponential phase, the sampling was performed 9 minutes after rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 9 minutes after rifampicin addition in kinetic 1

value: 9 minutes after rifampicin addition


title: prl1 prl2 Chomatin RNAseq rep2

value: prl1 prl2

value: rRNA-depleted Chromatin RNA


title: SO1


title: prl1 prl2  mRNAseq rep2

value: rRNA-depleted Total RNA


title: Ecoli_rne(ΔMTS)_T0_kinetic1

description:
Escherichia coli MG1667
Cells were in mid-exponential phase, the sampling was performed just before rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling before rifampicin addition in kinetic 1

value: before rifampicin addition


title: naked mole-rat spleen saline control sample 2 replicate 1

value: saline control

value: 23-25 months old


title: gfp_18hpf_2

city: New York

first: Lionel

last: Christiaen

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: New York University

data_processing:
ATAC-seq reads were trimmed using trim_galore version 0.4.4 with parameters --nextera --paired –three_prime_clip_R1 1 --three_prime_clip_R2 1
ATAC-seq reads were aligned using Bowtie2 version 2.3.2 with parameters –no-discordant --no-mixed -N 1 -X 1000
RNA-seq reads were aligned using STAR version 2.5.3a with parameters --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts TranscriptomeSAM --bamRemoveDuplicatesType UniqueIdentical
Reads were filtered to remove duplicates, mitochondrial reads, and quality score less than 30
ATAC-seq peaks were called using macs2 version 2.1.1 with gDNA as the input control and parameters  --nomodel -g 1.15e8 --keep-dup all --shift -29 --extsize 50 --bdg --call-summits
Genome_build: kh2013
Supplementary_files_format_and_content: bigWig files were generated using deepTools version 2.4.2 with parameters --centerReads --normalizeUsingRPKM --bs 10; Scores represent read density normalized by RPKM
Supplementary_files_format_and_content: Read counts for merged ATAC-seq peaks were generated using bedtools version 2.26.0
Supplementary_files_format_and_content: Read counts for RNA-seq were generated using HTSeq version 0.6.1p1 with parameters -r pos -i gene_id

organism: Ciona robusta

source_name: ASM+SHP+FHP

growth_protocol: Gametes from several Ciona adults were collected separately for in vitro cross-fertilization followed by dechorionation and electroporation. Electroporated eggs were cultured in filtered artificial seawaterin  agarose-coated plastic Petri dishes at 18°C.

extract_protocol:
Nulcei were isolated from FACSorted cells and incubated in the tagmentation reaction. Tagmented-chromatin fragmented were PCR amplified and purified. The quality of ATAC-seq libraries was assessed by using 2100 Bioanalyzer (Agilent Technologies).
ATAC-seq was performed with minor modifications to the published protocol (Buenrostro et al., 2013). 3000-5000 cells obtained by FACS were centrifuged at 800 x g for 4 min at 4 °C for each sample. Cells were resuspended in 5 µL of cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 nM NaCL, 3 nM MgCl2, 0,1% v/v Igepal CA-360 [Sigma-Aldrich] and incubated on ice for 5 min. After centrifugation of the cells at 500 x g for 10 min at 4 °C, the supernatant was discarded.  The tagmentation reaction was performed at 37 °C for 30 min using Nextera Sample Preparation kit (Illumina). After tagmentation, transposed DNA fragments were amplified using the following PCR condition: 1 cycle of 72°C for 5 min and 98°C for 30 s, followed by 12 to 14 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Amplified libraries were purified using PCR purification MinElute kit (Qiagen), and the quality of of the purified library was assessed by using 2100 Bioanalyzer (Agilent Technologies) and a High Sensitivity DNA analysis Kit (Agilent Technologies) to confirm a period pattern in the size of the amplified DNA. After size selection by using Agencourt Ampure XP beads (Beckman Coulter, Cat#A633880) with a bead-to-sample ratio of 1.8:1, the libraries were sequenced as paired-end 50 bp by using the HiSeq 2500 platform (Illumina) according to the manufacturer’s instructions. An input control was also generated by using 10 ng of C. robusta genomic DNA.

treatment_protocol: Different quantities of plasmids were electroporated depending on the constructs: the amount of fluorescent reporter DNA (Mesp>nls::lacZ, Mesp>hCD4::mCherry, Mesp>tagRFP, MyoD905>EGFP and Hand-r>tagBFP) and NLS::lacZ was typically 50 μg, but only 15 µg for Mesp-1>H2B::mCherry. For perturbation constructs (Mesp>Fgfr, Mesp>Mek, Foxf>M-RasCA, Hand-r>FgfrDN),  70 µg were usually electroporated, except for Mesp>nls::Cas9-Gem::nls (30 µg) and pairs of U6 >sgRNA plasmids (25 µg each).

value: control

tag: time

tag: cell lineage

value: mesenchyme

tag: omit

value: TRUE

tag: method

value: old

tag: ko

value: FALSE

tag: date


title: prl1 prl2 Chomatin RNAseq rep1


title: prl1 prl2  mRNAseq rep1


title: Pyruvate at 24 hours, Replicate 1

description: Ribosomal depleted total RNA

tag: strain


title: naked mole-rat spleen sample 4 replicate 1

tag: tissue

value: normal

value: male


title: naked mole-rat spleen saline control sample 1 replicate 2

value: single spleen cells


title: Pyruvate at 6 hours, Replicate 3

description: Ribosomal depleted total RNA

value: Pyruvate at 6 hours


title: WT Chomatin RNAseq rep2

tag: genotype/variation

value: wild type


title: WT mRNAseq rep2

tag: molecule


title: naked mole-rat spleen saline control sample 1 replicate 1

tag: condition


title: WT mRNAseq rep1


title: L-Lactate at 6 hours, Replicate 2

description: Ribosomal depleted total RNA

value: L-Lactate at 6 hours


title: Succinate RNA-seq Rep C

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description:
Succinate_3
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt

data_processing:
For the paired-end RNA-seq samples, only the R1 read was analyzed for consistency with the single-end RNA-seq samples.
Reads were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3, SLIDINGWINDOW of 3:30, and MINLEN of 36.
The trimmed reads were aligned to the R. palustris CGA009 genome sequence (GenBank assembly accession GCA_000195775.1) using Bowtie2 version 2.2.2 with default settings except the number of mismatches allowed was set to 1.
Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings except for the “reverse” strandedness argument was used.
DESeq2 version 1.22.2 was used to identify significantly differentially expressed genes from pairwise analyses, using a Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold and/or a fold change greater than two.
Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Genome_build: GCF_000195775.1_ASM19577v1
Supplementary_files_format_and_content: The data are given as RPKM values for each replicate and FDR for given comparisons from DESeq2.

organism: Rhodopseudomonas palustris

source_name: Single Isolate

growth_protocol: R. palustris was grown photosynthetically under anaerobic conditions (95% H2, 5% CO2) at 30°C until mid-log phase. RNA was harvested for immediate RNA extraction, no storage of cells.

extract_protocol:
Cells were harvested by transferring 10 ml of culture to an ice-cold 15-ml conical tube containing 1.25 ml of 5% water-saturated phenol in ethanol. Cells were collected by centrifugation at 5,000 × g for 5 min at 4°C, and the cell pellet was frozen in a dry ice-ethanol bath prior to storage at −80°C. The pellet was resuspended in 800 μl of 0.5 mg/ml lysozyme in TE (10 mM Tris-Cl [pH 8.0], 1 mM EDTA). Cells were lysed by the addition of 1/10 volume 10% sodium dodecyl sulfate and incubation at 64°C for 2 min. Next, 1/10 volume of 1 M sodium acetate, pH 5.2, was added, followed by extraction with an equal volume of water-saturated phenol. Samples were incubated at 64°C for 6 min with mixing every 30 s and then chilled on ice before centrifugation at 16,000 × g for 10 min at 4°C. The aqueous phase was removed and extracted with phenol a second time, followed by extraction with an equal volume of chloroform. To the final aqueous phase we added 1/10 volume 3 M sodium acetate (pH 5.2), 1 mM EDTA, and 2 to 2.5 volumes cold ethanol. The samples were incubated at −80°C for ≥20 min and centrifuged at 16,000 × g for 25 min at 4°C to collect the nucleic acids. The pellet was washed with ice-cold 80% ethanol, centrifuged for 5 min, and air dried, followed by resuspension in 86 μl of water.
Illumina TruSeq Strand Specific RNA-seq library prep was used following standard protocols.

tag: growth conditions

value: Anaerobic Photosynthetic Growth

tag: temperature

tag: carbon source

value: succinate


title: L-Lactate at 6 hours, Replicate 1

description: Ribosomal depleted total RNA

tag: treatment


title: Succinate RNA-seq Rep B

description:
Succinate_2
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt


title: Pyruvate at 24 hours, Replicate 2

description: Ribosomal depleted total RNA

value: Pyruvate at 24 hours


title: Bh_YL

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

description:
Expanding young leaves of 1-month-old Boea hygrometrica.
processed data file: Differentially methylated region.xlsx

data_processing:
RNA-seq: HISAT was used to perform genome mapping.
RNA-seq: StringTie v1.0.4 was used to reconstruct transcripts.
RNA-seq: Cuffcompare v2.2.1 was used to compare reconstructed transcripts to reference annotation.
RNA-seq: CPC v0.9-r2 was used to predict coding potential of novel transcripts.
RNA-seq: Bowtie2 v2.2.5 was used to map clean reads to reference.
Bisulfite-seq: BSMAP was used to map clean reads to reference with 2 forward strands.
Bisulfite-seq: Methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Bisulfite-seq: Putative DMRs were identified by comparison of the sample1 and sample2 methylomes using windows that contained at least 5 CpG (CHG or CHH) sites with a 2-fold change in methylation level and Fisher test p value <= 0.05.
Genome_build: GCA_001598015.1 (Boea_hygrometrica.v1)
Supplementary_files_format_and_content: Gene expression and annotation.xlsx: Excel file includes FPKM values for each sample.
Supplementary_files_format_and_content: Differentially methylated region.xlsx: Excel file includes details of differentially methylated CG, CHG and CHH regions between samples.

organism: Dorcoceras hygrometricum

source_name: young leaves

growth_protocol: Seeds of B. hygrometrica collected from wild plants growing in Beijing suburbs (China) were sterilized by immersion in 75% (v/v) ethanol solution for 1 min, followed by immersion in 10% (w/v) NaClO solution for 15 min and five times with sterile distilled water. Sterile seeds were vernalized at 4ºC in the dark for 3 days and then germinated on half-strength (1/2) MS medium supplemented with 1% sucrose and 0.6% agar under conditions of 16 h light/8 h dark at 25ºC for one week. No plant growth regulators (PGRs) were added. After germination, the seedlings were transferred to glass jars containing the same solid medium and continued to be cultured under the same environment condition.

value: young leaves

tag: developmental stage

value: untreated


title: naked mole-rat circulating immune cells sample 2

value: single circulating immune cells

tag: Sex

tag: age

value: 23-25 months old


title: naked mole-rat spleen sample 2 replicate 1

value: female


title: L-Lactate at 6 hours, Replicate 3

description: Ribosomal depleted total RNA


title: naked mole-rat spleen sample 4 replicate 2


title: naked mole-rat spleen sample 2 replicate 2


title: mac3a mac3b Chomatin RNAseq rep1

value: mac3a mac3b

value: rRNA-depleted Chromatin RNA


title: naked mole-rat spleen sample 1 replicate 2


title: Total RNAseq rep2

value: rRNA-depleted Total RNA


title: naked mole-rat spleen sample 3 replicate 2

value: normal


title: naked mole-rat spleen sample 3 replicate 1

value: male


title: WT Chomatin RNAseq rep1


title: Succinate RNA-seq Rep A

description:
Succinate_1
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt


title: mac3a mac3b Chomatin RNAseq rep2


title: Glucose at 6 hours, Replicate 3

description: Ribosomal depleted total RNA

value: Glucose at 6 hours


title: Syringic Acid RNA-seq Rep A

description:
SA_1
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt

value: syringic acid


title: L-Lactate at 24 hours, Replicate 1

description: Ribosomal depleted total RNA

value: L-Lactate at 24 hours


title: Syringic Acid RNA-seq Rep B

description:
SA_2
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt


title: Glucose at 6 hours, Replicate 2

description: Ribosomal depleted total RNA


title: L-Lactate at 24 hours, Replicate 2

description: Ribosomal depleted total RNA


title: L-Lactate at 24 hours, Replicate 3

description: Ribosomal depleted total RNA


title: GBM3565 CTCF ChIP-seq

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version  0.4.1.
Trimmed reads were alighed to hg19 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Peaks were called with MACS version 2.1.1 to define broad peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigWIG files were generated using bamCoverage with reads per genome coverage normalization. BED files in a narrowPeaks format from MACS2.

organism: Homo sapiens

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according previous methods (e.g. Schmidt et al. Methods 2009). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina MiSeq 500 following the manufacturer's protocols using 75 bp single end reads.

value: glioblastoma patient-derived cell model

tag: chip antibody

value: rabbit anti-CTCF (Cell Signaling #3418)


title: Syringic Acid RNA-seq Rep C

description:
SA_3
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt

value: Anaerobic Photosynthetic Growth


title: 4-HBA RNA-seq Rep B

description:
4-HBA_2
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt

value: 4-hydroxybenzoic acid


title: Total RNAseq rep1


title: naked mole-rat spleen sample 1 replicate 1

value: single spleen cells


title: GSC23 CTCF ChIP-seq


title: Total RNAseq rep3


title: 4-HBA RNA-seq Rep C

description:
4-HBA_3
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt


title: Chomatin RNAseq rep1


title: CD34+ cord blood cells, d2_UM171_35nM

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
CD34+ cord blood (CB) cells were cultured for 48h, a timepoint before most cells undergo division. Experimental conditions included either DMSO or two different UM171 concentrations; 35nM, a dose previously established as optimal for HSC expansion as well as 1000 nM. Single-cell RNAseq from each of these cultures was performed on a Chromium Single-Cell Controller (10X Genomics) using the Single Cell 3’ Reagent Kit version 2 according to manufacturer’s instructions. Target cell numbers were 6,000 per condition. Sequencing of the scRNAseq libraries was performed on an Illumina NovaSeq device using a S2 (PE 28x91) setup. A standard Cellranger v3.0.1 pipeline was used for read mapping (GRCh38 annotation) and demultiplexing. Subsequent analyses were done in Seurat (v2.3) and included (i) exclusion of cells with less than 1,000 genes or unique molecular identifiers (UMI), (ii) exclusion of cells with more genes or UMIs than the respective means plus 2 standard deviations (likely representing multiplets), (iii) exclusion of cells with more than 6% mitochondrial gene expression (representing apoptotic cells). Expression counts were log-normalized (scale factor 10,000) and scaled including regression on number of UMI’s, cell cycle scores and mitochondrial gene content. Multi-set Canonical Correlation Clustering and tSNE embedding was performed using variable genes (defined by mean.function = ExpMean, dispersion.function = LogVMR, x.low.cutoff = 0.02, x.high.cutoff = 5, y.cutoff = 2) excluding sex-specific genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix where each row contains normalized gene expression obtained from after applying normalization and scaling using the Seurat v2.3 processing pipeline.  Each column header contains the sample identifier and cell barcode identifier.

source_name: umbilical cord blood CD34+

growth_protocol: Human CD34+ cells were cultured in HSC expansion media consisting of StemSpan SFEM (StemCell Technologies) supplemented with human 100 ng/ml stem cell factor (SCF, R&D Systems), 100 ng/ml FMS-like trysine kinase 3 ligand (FLT3, R&D Systems), 50 ng/ml thrombopoietin (TPO, R&D Systems), and 10 μg/ml low-density lipoprotein (StemCell Technologies).

extract_protocol:
Single cells were processed using the 10X Chromium controlller.
10X Chromium version 2 3' RNAseq.
Illumina NovaSeq 6000 S2

treatment_protocol: CD34+ cultures were supplemented with either DMSO, 35 nM or 1000 nM UM171 (StemCell Technologies).

tag: cell type

value: CD34+ cord blood cells

tag: ex vivo culture


title: 4-HBA RNA-seq Rep A

description:
4-HBA_1
Grow in anaerobic culturing tube, harvest during exponential growth for immediate RNA extraction, no storage of cells.
processed data file: RPKM_normalized_data.txt


title: Z1

city: Harbin

first: Yanhua

state: China

address: College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang 150030, P.R. China

institute: Northeast Agricultural University

data_processing: De novo assembly, unigene annotation and functional classification  Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases  and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo  assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence  content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene'  sequence (aka Unigene).  All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology  (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)  (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of  Evalue<0.00001.  Differentially expressed Unigene analysis  Salmon [4] was used to perform expression level for Unigenes by calculating TPM [5]. The differentially expressed Unigenes were  selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [6].  Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.

organism: Syringa oblata

source_name: leaves

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and  purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10  ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads  (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under  elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the  protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was  300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's  recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 40% ~ 50% shading

value: leaves


title: HCT116_Protectseq_nanopore

city: Worcester

first: George

last: Spracklin

state: Massachusetts

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

data_processing:
FASTQ files were trimmed and assessed for quality with fastp.
Trimmed reads were mapped to hg38 (UCSC) using bwa mem.
Alignment files (BAM format) were filtered using encode_filter.py
Replicate filtered BAM files were merged using sambamba.
Signal tracks were generated using 100bp bins and normalized to reads per genomic coverage (RPGC) using deeptools bamcoverage with the following parameters: -bs 100 -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC -e.
Differential signal tracks (log2ratio) were generated using deeptools bamcompare. Published data (fastq files) were downloaded from GEO and processed as described above.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using deeptools. Scores represent as either log2ratio(signal/input) or reads per genomic content (RPGC). Domains (BED file) were called with HMMs.

growth_protocol: HCT116 and DKO cells were cultured in McCoy5A media. DKO cells were grown in the presence of G418, geneticin. HT1080 cells were cultured in DMEM media with L-glutamine. All media was supplemented with 10% FBS  at 37C/5%CO2

extract_protocol:
Cells were grown to ~75% confluency, harvested with trypsin, washed in 1X PBS, and frozen/stored at -80°C. Thawed cells were fixed in 1% formaldehyde and quenched in 0.125M Glycine, then washed twice in 1X PBS. Fixed cells were then resuspended in 500ul lysis buffer (50mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40, 1X PITC) for 30 min on ice with periodic resuspension.
Libraries were prepared using NEB UltraII DNA library kit

tag: cell line

value: colon cancer cell line

tag: cell line source gender

tag: library strategy

value: Protect-seq


title: Glucose at 24 hours, Replicate 2

description: Ribosomal depleted total RNA

tag: strain

value: Glucose at 24 hours


title: Z0

value: natural growth

tag: tissue


title: Chomatin RNAseq rep3

tag: molecule

value: rRNA-depleted Chromatin RNA


title: Chomatin RNAseq rep2


title: CD34+ cord blood cells, d2_DMSO

value: DMSO


title: Glucose at 6 hours, Replicate 1

description: Ribosomal depleted total RNA

value: Glucose at 6 hours


title: Glucose at 24 hours, Replicate 3

description: Ribosomal depleted total RNA


title: Nelfe_unt_2

status: Public on Nov 24 2019

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

data_processing:
HiSeq2500 (HiSeq Control Software version 2.2.58), Basecalling was done with CASAVA v1.8-4
Fastq files were mapped against GrCh37 using bowtie (v.1.1.2, -l 28 -n 2 -e 70 –best –strata –trim5 10). Postprocessing was done using samtools (v. 1.2)
after mapping mapped reads were extended to a fragment length of 200 and read depth normalised bigwig files were produced using bedtools (v2.25.0) and  UCSC tools, bigwig files were translated to ucsc genomes using a custom rscript
Genome_build: GRCh37
Supplementary_files_format_and_content: normalised bigwig tracks for extended reads

source_name: Human osteosarcoma cell line

growth_protocol: U2OS cells were obtained from ATCC and cultured in D-MEM medium supplemented with 10% fetal bovine serum, L-glutamine, penicillin and streptomycin.

extract_protocol:
U2OS cells were cross-linked in medium containing 1% formaldehyde for 10 min at room temperature, neutralized with 0.125 M glycine, scraped off and rinsed twice with PBS. Pellets were resuspended in 10 ml of buffer L1 (50 mM Hepes KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol, 5% NP-40, 0.25% Triton X-100) and incubated for 10 min at 4°C. Cells were spun down, resuspended in 10 ml of buffer L2 (200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 10 mM Tris pH 8.0) and incubated for 10 min at room temperature followed by centrifugation and resuspension in 900 μl buffer L3 (1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 10 mM Tris pH 8.0, 100 mM NaCl, 0.1% Na-deoxycholate, 0.17 mM N-lauroyl sarcosine, supplemented with protease inhibitors).
Library was prepared with Ovation Ultralow Library Systems v2  (NuGEN) according to manufacturer's instructions.

treatment_protocol: Exponentially growing U2OS cells were used for the analysis.

value: Human osteosarcoma cell line

value: NELFE, Milipore, Cat# ABE48


title: CD34+ cord blood cells, d2_UM171_1000nM


title: input_UNT_2


title: input_UNT


title: NELFE_unt_1


title: Glucose at 24 hours, Replicate 1

description: Ribosomal depleted total RNA


title: Blood_MI_D0 [hyb21214]

city: Leuven

first: Maarten

last: Vanhaverbeke

address: Herestraat 49 box 911

department: Cardiovascular Sciences

country: Belgium

institute: KU Leuven

hyb_protocol: A mixture of purified and fragmented biotinylated cDNA and hybridization controls (Affymetrix) was hybridized (16 hours at 45°C) on Affymetrix HTA 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: Chips were scanned using a GeneChip® scanner 3000 (Affymetrix)

data_processing: Raw data was preprocessed on the Affymetrix Expression Console 1.4.1.46 and normalized using Robust Multi-Array Average and Signal Space Transformation. Inter-array variability was adjusted by fitting a linear model. The normalized data was downstream analyzed using Bioconductor 3.1 for R version 3.2.2 3. A linear model was fit using the package limma 3.24.15 to determine differential expression between MI at the 2 different time points and stable controls.

label: biotin

source_name: whole blood

label_protocol: 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChipTM WT PLUS Reagent Kit for GeneChipTM Whole Transcript Expression Arrays

growth_protocol: Whole blood RNA from peripheral blood of patients.

extract_protocol: Total RNA extraction using PAXgene Blood miRNA kit, followed by ethanol purification.

value: whole blood

tag: patient diagnosis

value: MI

tag: time point


title: Blood_MI_Y1 [hyb21083]


title: Blood_MI_D30 [hyb21139]


title: Blood_MI_Y1 [hyb21084]


title: Blood_MI_Y1 [hyb21085]


title: Blood_MI_D0 [hyb21076]


title: Blood_MI_Y1 [hyb21086]


title: Blood_MI_D30 [hyb21138]


title: Blood_CAD_D0 [hyb21088]

value: CAD


title: Blood_MI_Y1 [hyb21087]


title: Blood_MI_D0 [hyb21140]


title: Blood_MI_D30 [hyb21077]


title: Blood_MI_Y1 [hyb21078]


title: Blood_CAD_D0 [hyb21080]


title: Blood_MI_D30 [hyb21091]


title: Blood_MI_D0 [hyb21093]


title: Blood_MI_Y1 [hyb21075]


title: Blood_MI_Y1 [hyb21070]


title: Blood_MI_D0 [hyb21071]


title: Blood_MI_Y1 [hyb21069]


title: Blood_MI_Y1 [hyb21068]


title: Blood_MI_D30 [hyb21072]


title: Blood_MI_Y1 [hyb21065]


title: Blood_MI_D0 [hyb21073]


title: Blood_CAD_D0 [hyb21079]


title: Blood_MI_Y1 [hyb21067]


title: Blood_MI_D30 [hyb21074]


title: Blood_MI_Y1 [hyb21066]


title: Blood_MI_Y1 [hyb21062]


title: Blood_MI_Y1 [hyb21063]


title: Blood_MI_Y1 [hyb21059]


title: Blood_MI_Y1 [hyb21092]


title: Blood_MI_Y1 [hyb21061]


title: Blood_MI_Y1 [hyb21058]


title: Blood_CAD_D0 [hyb21089]


title: Blood_MI_Y1 [hyb21048]


title: Blood_MI_Y1 [hyb21054]


title: Blood_MI_Y1 [hyb21057]


title: Blood_MI_Y1 [hyb21050]


title: Blood_MI_Y1 [hyb21064]


title: Blood_CAD_D0 [hyb21055]


title: Blood_MI_Y1 [hyb21052]


title: Blood_MI_Y1 [hyb21047]


title: Blood_MI_Y1 [hyb21053]


title: Blood_MI_Y1 [hyb21049]


title: Blood_MI_Y1 [hyb21041]


title: Blood_MI_D0 [hyb20834]


title: Blood_CAD_D0 [hyb20836]


title: Blood_MI_Y1 [hyb20841]


title: Blood_MI_Y1 [hyb21042]


title: Blood_MI_Y1 [hyb21046]


title: Blood_MI_D30 [hyb20827]


title: Blood_MI_Y1 [hyb21060]


title: Blood_MI_D30 [hyb20835]


title: Blood_MI_Y1 [hyb21045]


title: Blood_CAD_D0 [hyb20828]


title: Blood_CAD_D0 [hyb20831]


title: Blood_MI_Y1 [hyb21043]


title: Blood_MI_Y1 [hyb21044]


title: Blood_CAD_D0 [hyb20837]


title: Blood_MI_D30 [hyb20839]


title: Blood_MI_Y1 [hyb20840]


title: Blood_MI_D0 [hyb20838]


title: Blood_MI_D30 [hyb20823]


title: Blood_MI_D0 [hyb20832]


title: Blood_MI_D30 [hyb20833]


title: Blood_CAD_D0 [hyb20830]


title: Blood_MI_D0 [hyb20812]


title: Blood_MI_D0 [hyb20822]


title: Blood_CAD_D0 [hyb21056]


title: Blood_MI_D30 [hyb20815]


title: Blood_MI_D30 [hyb20817]


title: Blood_MI_D0 [hyb20808]


title: Blood_MI_D30 [hyb20825]


title: Blood_MI_D0 [hyb20824]


title: Blood_MI_D0 [hyb20826]


title: Blood_MI_D30 [hyb20819]


title: Blood_CAD_D0 [hyb20806]


title: Blood_MI_D0 [hyb20820]


title: Blood_CAD_D0 [hyb20829]


title: Blood_MI_D0 [hyb20816]


title: Blood_MI_D0 [hyb20802]


title: Blood_MI_D30 [hyb20821]


title: Blood_MI_D30 [hyb20813]


title: Blood_MI_D30 [hyb20799]


title: Blood_MI_D30 [hyb20811]


title: Blood_MI_D30 [hyb20803]


title: Blood_MI_D0 [hyb20800]


title: Blood_MI_D0 [hyb20796]


title: Blood_MI_D0 [hyb20794]


title: Blood_MI_D30 [hyb20809]


title: Blood_MI_D30 [hyb20793]


title: Blood_MI_D0 [hyb20810]


title: Blood_CAD_D0 [hyb20807]


title: Blood_MI_D0 [hyb20790]


title: Blood_MI_D30 [hyb20791]


title: Blood_MI_D0 [hyb20792]


title: Blood_CAD_D0 [hyb20804]


title: Blood_MI_D0 [hyb20798]


title: Blood_MI_D30 [hyb20801]


title: Blood_CAD_D0 [hyb20805]


title: Blood_MI_D30 [hyb20797]


title: Blood_MI_D0 [hyb20784]


title: Blood_MI_D0 [hyb20782]


title: Blood_MI_D30 [hyb20783]


title: Blood_MI_D0 [hyb20786]


title: Blood_MI_D30 [hyb20779]


title: Blood_CAD_D0 [hyb20780]


title: Blood_MI_D30 [hyb20795]


title: Blood_MI_D30 [hyb20775]


title: Blood_MI_D30 [hyb20785]


title: Blood_MI_D30 [hyb20787]


title: Blood_MI_D0 [hyb20778]


title: Blood_MI_D0 [hyb20770]


title: Blood_MI_D0 [hyb20768]


title: Blood_CAD_D0 [hyb20781]


title: Blood_MI_D0 [hyb20772]


title: Blood_MI_D30 [hyb20777]


title: Blood_MI_D0 [hyb20788]


title: Blood_MI_D0 [hyb20766]


title: Blood_MI_D0 [hyb20774]


title: Blood_MI_D30 [hyb20769]


title: Blood_MI_D30 [hyb20771]


title: Blood_MI_D30 [hyb20773]


title: Blood_MI_D0 [hyb20764]


title: Blood_MI_D30 [hyb20767]


title: Blood_MI_D30 [hyb20763]


title: Blood_MI_D0 [hyb20762]


title: Blood_CAD_D0 [hyb20759]


title: Blood_MI_D30 [hyb20761]


title: Blood_MI_D0 [hyb20760]


title: Blood_MI_D30 [hyb20753]


title: Blood_MI_D0 [hyb20754]


title: Blood_MI_D0 [hyb20748]


title: Blood_CAD_D0 [hyb20757]


title: Blood_MI_D0 [hyb20744]


title: Blood_CAD_D0 [hyb20758]


title: Blood_MI_D30 [hyb20765]


title: Blood_MI_D30 [hyb20749]


title: Blood_CAD_D0 [hyb20756]


title: Blood_MI_D0 [hyb20750]


title: Blood_MI_D0 [hyb20740]


title: Blood_MI_D30 [hyb20745]


title: Blood_MI_D30 [hyb20751]


title: Blood_MI_D0 [hyb20814]


title: Blood_MI_D0 [hyb20736]


title: Blood_MI_D30 [hyb20755]


title: Blood_MI_D30 [hyb20747]


title: Blood_MI_D30 [hyb20741]


title: Blood_MI_D0 [hyb20738]


title: Blood_MI_D0 [hyb20742]


title: Blood_MI_D0 [hyb20746]


title: Blood_MI_D0 [hyb20818]


title: Blood_MI_D0 [hyb18788]


title: Blood_MI_D0 [hyb20776]


title: Blood_MI_D30 [hyb18785]


title: Blood_MI_D30 [hyb20737]


title: Blood_MI_D0 [hyb18782]


title: Blood_MI_D30 [hyb18787]


title: Blood_MI_D30 [hyb18781]


title: Blood_MI_D30 [hyb18769]


title: Blood_MI_D0 [hyb18784]


title: Blood_MI_D0 [hyb18786]


title: Blood_MI_D30 [hyb18789]


title: Blood_MI_D0 [hyb18766]


title: Blood_MI_D30 [hyb18783]


title: Blood_MI_D0 [hyb18768]


title: Blood_MI_D30 [hyb18777]


title: Blood_MI_D0 [hyb18770]


title: Blood_MI_D0_Techn_Repl_of_hyb20782 [hyb18778]


title: Blood_MI_D30 [hyb18765]


title: Blood_MI_D0 [hyb18776]


title: Blood_MI_D30 [hyb18767]


title: Blood_MI_D0 [hyb18772]


title: Blood_MI_D30 [hyb18771]


title: Blood_MI_D30 [hyb20789]


title: Blood_MI_D30_Techn_Repl_of_hyb20783 [hyb18779]


title: Blood_MI_D0 [hyb18780]


title: Blood_MI_D0 [hyb18764]


title: Blood_MI_D0 [hyb18762]


title: Blood_MI_D30 [hyb18763]


title: Blood_MI_D30 [hyb18773]


title: MG_Human_PMNC_LTA_pep2c_hPMNC_cell_only_3

city: Rehovot

first: Steffen

last: Jung

address: 234 Herzl Street

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

description: Single read (read2 used to read sample barcodes and UMI only)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
For example: the UMI GTACTGGT will appear in the following format: @NB501465:106:HFFKNBGX2:1:11101:5035:1075:AGGCTAAGTACTGGT:A6/A/E//EE////E:0
alignment: hisat 0.1.6  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) located in fastq header.
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Samples were suspended and incubated in staining medium (PBS without calcium and magnesium with 2% heat-inactivated Fetal Calf/Bovine Serum (FCS/FBS) and 1mM EDTA) containing fluorescent antibodies. Following incubation, cells were washed with staining buffer only or staining buffer with DAPI, centrifuged, filtered through 80μm filter and read. Sorting was performed on FACSAria III or FACSAria Fusion (BD Biosciences).
Blood was retrieved from healthy participants and added to 60% Dextran solution (6% Dextran T-500 (Sigma) in PBS++, pH 7.4) and 40% Citrate buffer (5% Na Citrate + 1.6% Citric acid in PBS++). To isolate peripheral blood mononuclear cells, mixture was left for 30 minutes in room temperature and supernatant was collected and loaded on Ficoll. Tubes were centrifuged in 920 g in 8oC for 25 minutes without breaks and interphase were collected and washed with cold PBS. Pellet was suspended and filtered with a 70μm filter. Cells were washed with MACS buffer (PBS with 0.5% BSA and 2mM EDTA), counted and incubated in MACS buffer with 1:10 CD14 microbeads (Miltenyi Biotech), 100μl for 107 cells. CD14+ cells were isolated by MACS magnetic column (Miltenyi Biotech) according to manufacturer's instructions. Cells were seeded on 24-well tissue culture plates, 1x105 cells per well in RPMI medium (Biological industries) with 20% heat-inactivated fetal bovine serum (FBS) (Life technologies), 1% penicillin streptomycin amphotericin b solution (Biological industries), 1% L-Glutamine (Biological industries). After 3 days, half the medium was renewed. Cells were analyzed on day 7.
RNA-seq of populations was performed as described previously (Lavin 2014)

treatment_protocol: Mice were given 1.5% dextran sulfate sodium (DSS; TdB) in the drinking water for 7 days. Peptides were dissolved in saline and injected every other day starting from day 1 of DSS. Control mice received regular water and injected with saline, DSS Only mice were injected with saline.

tag: organ

value: Colon

tag: isolation

value: Ficoll, CD14 microbeads

tag: selection marker


title: MG_Human_PMNC_LTA_pep2c_hPMNC_LTA_only_2


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_5_1


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_5_3


title: MG_Human_PMNC_LTA_pep2c_hPMNC_cell_only_1


title: MG_Human_PMNC_LTA_pep2c_hPMNC_LTA_only_1


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_20_3


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_5_2


title: MG_Human_PMNC_LTA_pep2c_hPMNC_LTA_only_3


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_10_3


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_20_1


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_20_2


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_10_2


title: MG_Kamin_DSS6_WT_Mono_3.M

organism: Mus musculus

tag: genotype

value: C57BL/6J wildtype

value: Cell sorting

tag: dss treatment

value: treated and non-treated controls

tag: treatment

value: DSS 1.5% in drinking water


title: MG_Kamin_DSS6_WT_Mono_2.M


title: MG_Kamin_DSS6_WT_Mono_1.M


title: Blood_MI_D30 [hyb18761]


title: Blood_MI_D0_Techn_Repl_of_hyb20838 [hyb18756]


title: Blood_MI_D30 [hyb18759]


title: MG_Kamin_DSS6_WT_MF_2.M


title: Blood_MI_D0 [hyb18760]


title: Blood_MI_D30_Techn_Repl_of_hyb20839 [hyb18757]


title: Blood_MI_D0 [hyb18758]


title: Blood_MI_D30 [hyb18755]


title: Blood_MI_D0 [hyb18754]


title: Blood_MI_D0 [hyb18752]


title: MG_Kamin_DSS6_WT_MF_1.M


title: MG_Kamin_DSS6_WT_MF_3.M


title: MG_Kamin_DSS6_Scr_MF_2.M


title: MG_Human_PMNC_LTA_pep2c_hPMNC_2c_10_1


title: MG_Kamin_DSS6_DSS_Mono_3.M


title: MG_Kamin_DSS6_Scr_MF_4.M


title: MG_Kamin_DSS6_Scr_Mono_1.M


title: MG_Kamin_DSS6_Scr_Mono_4.M


title: MG_Kamin_DSS6_KD_Mono_4.M


title: MG_Kamin_DSS6_Scr_MF_1.M


title: MG_Kamin_DSS6_KD_MF_2.M


title: MG_Kamin_DSS6_DSS_Mono_4.M


title: MG_Kamin_DSS6_DSS_MF_4.M


title: MG_Kamin_DSS6_DSS_Mono_2.M


title: MG_Kamin_DSS6_KD_Mono_2.M


title: MG_Kamin_DSS6_DSS_MF_3.M


title: MG_Kamin_DSS6_KD_MF_4.M


title: MG_Kamin_DSS6_DSS_MF_2.M


title: MG_Kamin_DSS5_WT2_Mono.M


title: MG_Kamin_DSS6_Scr_Mono_2.M


title: MG_Kamin_DSS6_DSS_MF_1.M


title: MG_Kamin_DSS5_WT1_MF.M


title: MG_Kamin_DSS5_WT2_MF.M


title: MG_Kamin_DSS5_WT1_Mono.M


title: MG_Kamin_DSS5_Scr4_Mono.M


title: MG_Kamin_DSS5_Scr4_MF.M


title: MG_Kamin_DSS5_Scr3_Mono.M


title: MG_Kamin_DSS6_DSS_Mono_1.M


title: MG_Kamin_DSS5_Scr3_MF.M


title: MG_Kamin_DSS5_Scr2_Mono.M


title: MG_Kamin_DSS5_KD4_MF.M


title: MG_Kamin_DSS5_KD4_Mono.M


title: MG_Kamin_DSS5_KD3_MF.M


title: MG_Kamin_DSS5_KD3_Mono.M


title: MG_Kamin_DSS5_KD2_Mono.M


title: MG_Kamin_DSS5_KD1_Mono.M


title: MG_Kamin_DSS5_DSS1_MF.M


title: MG_Kamin_DSS5_DSS3_MF.M


title: MG_Kamin_DSS3_WT_3_MF


title: MG_Kamin_DSS5_KD1_MF.M


title: MG_Kamin_DSS3_WT_3_Mon


title: MG_Kamin_DSS3_WT_2_Mon


title: MG_Kamin_DSS3_WT_1_Mon


title: MG_Kamin_DSS3_KD_23_Mon


title: MG_Kamin_DSS3_KD_23_MF


title: MG_Kamin_DSS3_WT_1_MF


title: MG_Kamin_DSS5_Scr2_MF.M


title: MG_Kamin_DSS5_KD2_MF.M


title: MG_Kamin_DSS5_DSS3_Mono.M


title: RNA-seq_P3_WT4

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
The RNA-seq data was analyzed with bcbio-nextgen (https://github.com/chapmanb/bcbio-nextgen). Fastq files were aligned to the mm10 genome using STAR (Dobin et al., 2013, DOI:10.1093/bioinformatics/bts635). Transcript expression levels were estimated with Salmon (Patro et al., 2017, DOI: 10.1038/nmeth.4197). FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for QC metrics, and multiqc (Ewels et al., 2016, DOI: 10.1093/bioinformatics/btw354) for reporting. Data analysis was then performed with R/Bioconductor (https://www.R-project.org/, Gentleman et al. (2004, DOI: 10.1186/gb-2004-5-10-r80)). For the differential gene expression, we followed the recommendations from Soneson et al. (2015, DOI: 10.12688/f1000research.7563.2). Gene expression levels were assessed by adding all the transcript levels for a given gene and normalization of the counts was done with the lengthScaledTPM function of the tximport package followed by a limma-voom procedure: for each population (P1-3), genes with CPM>1 in at least 2 samples were selected, the TMM normalization was run using the calcNormFactors function of the limma package (Ritchie et al., 2015, DOI: 10.1093/nar/gkv007), and a linear model with Erg∆/∆ vs. Ergfl/fl was fitted (voom / lmFit / eBayes). P-values were adjusted using the Benjamini-Hochberg procedure.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet containing differential expression analysis, Erg fl/fl;CD2iCre (KO) vs. Erg fl/fl (WT). A separate tab is provided for the analysis of each of the three progenitor populations (P1, P2, P3) and an additional tab explains the content of each column.

growth_protocol: Cells FACS-sorted from freshly harvested murine bone marrow

extract_protocol:
Murine progenitor B-cells were FACS-sorted into RLT plus buffer (Qiagen) with 2-mercaptoethanol (Sigma-Aldrich, 10µl/mL RLT buffer).  The RNA was extracted with Qiagen’s AllPrep micro kit.
cDNA was obtained using the NuGEN’s Ovation RNA-seq System V2, and libraries were prepared with NuGEN’s Ovation Ultralow System V2. All according to manufacturer’s instructions. The samples were subjected to 75-cycles sequencing on an Illumina NextSeq 500 instrument.

tag: strain background

tag: genotype/variation

value: Erg fl/fl

value: Bone marrow

value: Progenitor B-cells

tag: progenitor cell type


title: MG_Kamin_DSS3_DSS_12_MF


title: MG_Kamin_DSS3_KD_15_MF


title: MG_Kamin_DSS3_DSS_22_Mon


title: MG_Kamin_DSS3_DSS_12_Mon


title: RNA-seq_P3_WT2

tag: cell type


title: RNA-seq_P3_KO4

value: Erg fl/fl;CD2iCre


title: MG_Kamin_DSS3_DSS_25_MF


title: MG_Kamin_DSS3_DSS_21_MF


title: MG_Kamin_DSS3_DSS_21_Mon


title: MG_Kamin_DSS3_DSS_22_MF


title: RNA-seq_P3_WT3


title: MG_Kamin_DSS3_DSS_13_Mon


title: MG_Kamin_DSS3_DSS_25_Mon


title: Tardbp_KO_rep4

city: Kunming

first: Baowei

last: Jiao

state: Yunnan

address: 32 Jiaochang Donglu Kunming

department: Kunming Institute of Zoology

description:
total RNA from mammary gland of Tardbp KO
s13-4804_H5FCJCCXY_L4

data_processing:
RNA-seq: Reads were aligned to the mm9 genome assembly using STAR_2.5.2a_modified; expression value were calculated using Version 1.4.6-p5 with the following configurations: -T 5 -a $gtf2 -t exon
Genome_build: Mouse NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Tardbp_KO, mammary gland

extract_protocol:
The mammary gland tissues were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland

value: Tardbp KO


title: MG_Kamin_DSS3_DSS_13_MF


title: RNA-seq_P3_WT1


title: Tardbp_KO_rep3

description:
total RNA from mammary gland of Tardbp KO
s12-4692_H5FCJCCXY_L4


title: Tardbp_KO_rep2

description:
total RNA from mammary gland of Tardbp KO
s10-4212_H5FCJCCXY_L5


title: Tardbp_KO_rep1

description:
total RNA from mammary gland of Tardbp KO
s6-4332_H5FCJCCXY_L1


title: WT_rep3

description:
total RNA from mammary gland of WT
s4-4315_H5FCJCCXY_L2

source_name: WT, mammary gland

value: WT


title: MG_Kamin_DSS3_KD_15_Mon


title: MG_Kamin_DSS3_WT_2_MF


title: RNA-seq_P3_KO3


title: RNA-seq_P3_KO1


title: WT_rep2

description:
total RNA from mammary gland of WT
s3-4805_H5FCJCCXY_L4


title: RNA-seq_P2_WT4


title: WT_rep1

description:
total RNA from mammary gland of WT
s1-4685_H5FCJCCXY_L3


title: RNA-seq_P2_WT1


title: RNA-seq_P2_WT2


title: RNA-seq_P2_WT3


title: PolII_p38iUV_5

treatment_protocol: U2OS cells were either mock-treated, irradiated with UV light (40 J/m2, 1 hour recovery) or pre-treated with 10 µM of p38 inhibitor SB203580 (Selleckchem) for 1-hour prior to irradiation with UV light (40 J/m2, 1 hour recovery).

tag: cell line

value: Human osteosarcoma cell line

tag: treated with

value: pre-treated with 10 µM of SB203580 for 1hr prior to irradiation with UV light (40 J/m2, 1 hour recovery)

tag: chip antibody

value: Pol II (N-20), Santa Cruz, Cat# sc-899


title: RNA-seq_P3_KO2

tag: tissue


title: RNA-seq_P2_KO4


title: PolII_UV_5

value: UV light (40 J/m2, 1 hour recovery)


title: RNA-seq_P2_KO3


title: RNA-seq_P2_KO2


title: RNA-seq_P2_KO1


title: PolII_UNT_5

value: mock


title: input_PolII_p38iUV_5


title: RNA-seq_P1_WT4


title: ATAC_KO4

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
ATAC-seq reads were aligned to the mm9 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept.
Regions enriched for open chromatin were identified using the ENCODE IDR (LI Q H, et al. 2011. Annals of Applied Statistics, 5:1752-1779) pipeline and MACS2 peak caller (Zhang Y, et al. 2008. Genome Biology 9:R137). Peak reproducibility was assesed between all 4 replicates yielding 6 IDR analyses. Reproducible peaks were defined by a p-value below 0.05 in at least 4 out of the 6 IDR analyses. Peak files with reproducible ATAC-seq sites of WT and KO progenitor B-cells were merged using Homer with distance option -d given.
ATAC-seq signal was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -noadj. Normalization of sequencing reads was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking replicates into the design matrix.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were created using HOMER for visualization of enhancer features in genome browser. Bed files contain reproducible genomic regions from IDR analysis of ATAC-seq experiments. Txt file contains non-adjusted ATAC-seq read density for each replicate as well as FDR and Log2FC with respect to wildtype cells.

source_name: ATAC_KO_FACS-sorted progenitor B-cells

growth_protocol: Cells were FACS-sorted from freshly harvested murine bone marrow

extract_protocol:
ATAC-seq was performed on 10,000 sorted progenitor B-cells as previously described (Buenrostro J D, et. al 2015. Current Protocols in Molecular Biology 109: 1-9). Sorted cells were permeabilized and exposed to 0.5µl transposase.
ATAC-seq libraries were constructed using the Nextera DNA library Prep kit (Illumina) according to the instructions by the manufacturer, and sequencing was performed on a HiSeq 1500 Illumina machine.

tag: cell subtype


title: input_PolII_UV_5


title: MG_Human_PMNC_LTA_pep2c_hPMNC_cell_only_2

value: Colon

value: Ficoll, CD14 microbeads


title: input_PolII_UNT_5


title: ATAC_KO2


title: RNA-seq_P1_WT2


title: input_PolII_p38iUV_4


title: SLB_3

city: Lan Zhou

first: Wei

last: Xiao

state: Gan Su

address: No. 1, Ying Men Village, Anning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

description: Transcript_length.txt,Transcript_n55.txt,FPKM_interval.txt,merged_fpkm.txt

data_processing:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Supplementary_files_format_and_content: Transcript_length.txt (The length of the  transcripts obtained by splicing)
Transcript_n50.txt (distribution table  of the  transcripts obtained by splicing)
FPKM_interval.txt (A statistical table of FPKM values for all samples)
merged_fpkm.txt (A list of FPKM values for all samples)

organism: Silurus lanzhouensis

source_name: SLB, muscle

growth_protocol: The ﬁsh were reared for 16 wk prior to challenge in an experimental tank(diameter 1.2m, and depth 1.5m).Tanks were set up with a constant ﬂow-through system (0.5 l/s) with fresh pond water at oxygen levels (8.0–10.0 ppm) and ambient temperature (～24°C).

extract_protocol:
Muscle was withdrawn from the back of the ﬁsh (1.5–2.0g) for RNA extraction. Tissues were placed into RNAlater, and then moved to -80°C for storage until use.Muscle was chosen for this study because of their essential physiological roles in respone to growth
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Meanwhile,accroding to the growth trait of S. lanzhouensis, The heaviest three fish and the lightest three fish from the tank were selected and divided into SLA and SLB.Fish sizes are key index focused in family selection of Silurus lanzhouensis(Figure1 and Table1.). Thus,before sampling ﬁsh were euthanized with MS-222 (300 mg/l) and then weighed and measured for body weight,total length,body height,head length,tail length.

tag: weight

value: lightest

value: muscle

tag: culturing time

value: 16 wk


title: RNA-seq_P1_WT1

value: Erg fl/fl


title: ATAC_KO1

value: Bone marrow


title: SLB_2

description: Transcript_length.txt,Transcript_n54.txt,FPKM_interval.txt,merged_fpkm.txt


title: SLB_1

description: Transcript_length.txt,Transcript_n53.txt,FPKM_interval.txt,merged_fpkm.txt


title: RNA-seq_P1_KO4

value: Progenitor B-cells


title: ATAC_WT4

source_name: ATAC_WT_FACS-sorted progenitor B-cells


title: R. mucilaginosa treated_24hrs Rice Roots, Replicate 1

city: Kolkata

first: Anindita

last: Seal

state: West Bengal

address: 35, Ballygunge Circular Road

department: Biotechnology

country: India

institute: University of Calcutta

description: Gene expression data from R. mucilaginosa treated (24hrs) rice root.

hyb_protocol: Hybridization was performed using GeneChip® Hybridization, Wash and Stain Kit as per manual (Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip® 3000 7G scanner.

data_processing: Raw data were analyzed using Expression Console tool, Affymetrix TAC software and Genesis tool. The background adjustment, Quantile normalization and summarization were done with the default setting of RMA16 algorithm followed by data adjustment and background correction in GENESPRING tool.

label: Biotin

organism: Oryza sativa

source_name: Rice root, R. mucilaginosa treated, 24hrs

label_protocol: Biotinylated cRNA were prepared according to GeneChip® WT Terminal Labeling Kit manual (Affymetrix).

extract_protocol: Total RNA was isolated from rice root tissues using HiPurATM Plant and Fungal RNA Miniprep Purification Spin Kit (Himedia, India).

treatment_protocol: Three-week-old rice plant grown in untreated condition were supplemented with Rhodototorula cell suspension. Roots were harvested 0hr, 6hrs or 24hrs post treatment.

tag: cultivar

value: Swarna MTU7029

value: Root

tag: age

value: 3 weeks

value: Rhodotorula mucilaginosa JGTA-S1

tag: time


title: Gene_expr_microarray_WT1

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturers specifications

scan_protocol: Standard Affymetrix protocol

data_processing: Cell intensity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA). Data from the microarrays was normalized using RMA (Bioconductor) (Gautier et al., 2004, DOI:10.1093/bioinformatics/btg405).

label_protocol: 2.5ug of amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions.

extract_protocol: Progenitor B-cells were sorted into RLT plus buffer (Qiagen) with 2-mercaptoethanol (Sigma-Aldrich, 10µl/mL RLT buffer).  Total RNA was extracted using the RNeasy micro kit (Qiagen), and libraries were obtained using the Ovation Pico WTA system V2 (NuGEN) following manufacturer’s instructions.


title: Gene_expr_microarray_KO3

value: Erg fl/fl;CD2iCre


title: RNA-seq_P1_WT3


title: Control Rice Roots, Replicate 1

description: Gene expression data from control rice root.

source_name: Rice root, control


title: Gene_expr_microarray_WT2


title: R. mucilaginosa treated_6hrs Rice Roots, Replicate 1

description: Gene expression data from R. mucilaginosa treated (6hrs) rice root.

source_name: Rice root, R. mucilaginosa treated, 6hrs


title: input_PolII_UNT_4

value: Human osteosarcoma cell line


title: Control Rice Roots, Replicate 2


title: SLA_3

description: Transcript_length.txt,Transcript_n52.txt,FPKM_interval.txt,merged_fpkm.txt

source_name: SLA, muscle

value: heaviest


title: R. mucilaginosa treated_24hrs Rice Roots, Replicate 2


title: ATAC_KO3


title: RNA-seq_P1_KO3


title: Gene_expr_microarray_KO2


title: R. mucilaginosa treated_6hrs Rice Roots, Replicate 2


title: ATAC_WT3


title: Gene_expr_microarray_KO1


title: input_PolII_UV_4

value: UV light (40 J/m2, 1 hour recovery)


title: Blood_MI_D30 [hyb18753]

value: whole blood

tag: patient diagnosis

value: MI

tag: time point


title: PolII_p38iUV_4

value: pre-treated with 10 µM of SB203580 for 1hr prior to irradiation with UV light (40 J/m2, 1 hour recovery)

value: Pol II (N-20), Santa Cruz, Cat# sc-899


title: PolII_UV_4


title: SLA_1

description: Transcript_length.txt,Transcript_n50.txt,FPKM_interval.txt,merged_fpkm.txt

value: muscle


title: ATAC_WT2


title: Gene_expr_microarray_WT3


title: NSG control

status: Public on Nov 23 2019

city: New Haven

first: Kofi

last: Mensah

state: CT

address: 300 George Street

department: Rheumatology, Allergy and Clinical Immunology

institute: Yale University School of Medicine

description: Human bone marrow B cells developed in NSG humanized mice after transplant with human hematopoietic stem cells

data_processing:
Illumina CASAVA v. 1.8.2
After sequencing, the analysis was performed using the proprietary RNAv9 pipeline platform from EA|Q2 Solutions
Genome_build: hg19
Supplementary_files_format_and_content: expanded matrix of RNA fragment counts per gene, including coverage estimates, detection calls

source_name: Human bone marrow B cells

extract_protocol: Bone marrow cells were flushed from the NSG mice and 150,000 cells were sorted for CD19+CD10+IgM+ B cells and then flash frozen on dry ice. RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

treatment_protocol: NSG mice NSG1+ATMi and NSG2+ATMi were injected with 10 mg/kg KU55933 ATM inhibitor for 10 days at 12 weeks of age after being transplanted with human stem cells at 2 days of age. NSG control as injected with DMSO vehicle at 12 weeks of age after being transplanted with human stem cells at 2 days of age.

value: Sorted human B cells flushed from NSG humanized mouse bone marrow

tag: agent


title: NSG2 ATMi

value: ATM inhibitor KU55933


title: NSG1 ATMi


title: SLA_2

description: Transcript_length.txt,Transcript_n51.txt,FPKM_interval.txt,merged_fpkm.txt

value: 16 wk


title: RNA-seq_P1_KO1

tag: strain background

value: Bone marrow

value: Progenitor B-cells


title: RNA-seq_P1_KO2

tag: genotype/variation


title: ATAC_WT1

value: Erg fl/fl


title: HT CsA 24h r1

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay according to manufacturer's protocol

scan_protocol: Illumina BeadArray Reader with DirectHyb Gene Expression scan settings

data_processing: The preprocessing pipeline was implemented in Mathworks MATLAB(R) and works similar to preprocessing Affymetrix CEL files: Measured gene expressions were imported on raw bead level (cf. supplementary TXT files). All microarrays were preprocessed and normalized together. Their intensity distributions for all measured beads were equalized by quantile normalization. The background mode was fitted and removed and a spot filter was applied to exclude too dim beads (< mean background intensity). Intensities were log2-transformed and aggregated by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer’s annotations. For genes having multiple beadsets the one with the highest expression (in average over all arrays) was selected.

source_name: cell line HT

label_protocol: RNA was transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol

growth_protocol: Both cell lines, HT and HBL-1, were  maintained in RPMI1640 medium with penicilin, streptomycin and plasmocin at 37°C with 5% CO2.  Whereas the medium for HT contained 10% FCS, HBL-1 were cultured in medium with 20% FCS.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer's protocol

treatment_protocol: The cell lines HBL-1 and HT were treated with 600 nM cyclosporin A or with DMSO for the indicated times.

tag: treatment

value: CsA

tag: duration in hours

tag: replicate


title: HT CsA 24h r3


title: HT CsA 12h r1


title: HT CsA 36h r2


title: HT DMSO 0h r1

value: DMSO


title: HT CsA 36h r1


title: HBL1 CsA 36h r2

source_name: cell line HBL1


title: HBL1 CsA 48h r1


title: HT DMSO 0h r2


title: HBL1 CsA 24h r2


title: HT CsA 36h r3


title: HBL1 CsA 36h r3


title: HT DMSO 0h r3


title: HT CsA 12h r3


title: HBL1 CsA 48h r2


title: HT CsA 12h r2


title: HBL1 CsA 48h r3


title: HT CsA 24h r2


title: HBL1 CsA 36h r1


title: HBL1 CsA 12h r3


title: HBL1 DMSO 0h r2


title: HBL1 DMSO 0h r1


title: HBL1 CsA 24h r1


title: HBL1 CsA 12h r2


title: HBL1 DMSO 0h r3


title: HBL1 CsA 12h r1


title: Evolved 3

city: Bogotá

first: Albert

middle: Enrique

last: Tafur Rangel

address: Cra 1 Nº 18A - 12 Edificio ML

department: Chemical and Food Engineering

country: Colombia

institute: Universidad de Los Andes

description:
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Evolved_3

data_processing:
Evaluate sequence quality.
Trimm reads by using trimmomatic v 0.38.
Map reads to genome RefSeq Escherichia coli ATCC 8739 using bowtie2.
Counts by using featureCounts.
SARTools (Statistical Analysis of RNA-Seq data Tools) was used for statistical RNA-Seq analysis. Differentially expressed genes (DEGs) were identified by using the DESeq2 R Package.
Genome_build: NC_010468.1
Supplementary_files_format_and_content: Supplementary_file_S1.xlsx: Excel file with normalized counts and differential expression.

organism: Escherichia coli

source_name: bacterial total RNA

growth_protocol: To compare the global gene expression profiles between cells grown in an optimized culture medium (condition 3) and one evolved strain. Triplicates of E. coli ATCC 8739 were grown in a glycerol-based medium containing 5 g/L yeast extract, 2.5 g/L NaCl, 5mL/L trace metals solution (0.55 g/L CaCl2, 0.10 g/L MnCl2 4H2O, 0.17 g/L ZnCl2, 0.043 g/L CuCl2 2H2O, 0.06 g/L CoCl2 6H2O, 0.06 g/L Na2MoO4 2H2O, 0.06 g/L Fe(NH4)2(SO4)2 6H2O, 0.20 g/L FeCl3 6H2O), 5 mL/L MgSO4 1M, 30 g/L glycerol for the reference conditions (Condition 11). Condition 3 and evolved strain were grown in triplicates in the glycerol-based medium supplemented with 1g/L of NH4Cl, 6 g/L of Na2HPO4, and 3 g/L of K2HPO4. All the cultures were carried out at 37°C and 200 rpm in 250 ballfed Erlenmeyer containing 50 ml of culture medium.

extract_protocol:
The Qiagen RNeasy Mini kit (Cat No./ID: 74104) was used to obtain total RNA for further analysis according to the manufacturer’s protocol. Each sample was treated with DNase in order to remove the genomic DNA.
Genewiz protocol. Whole transcriptome sequencing via rRNA depletion.

treatment_protocol: In order to harvest the cells to purify RNA after six h of culture, sample were first treated with RNAprotect bacterial reagent (Cat No./ID: 76506) and enzymatic lysis and Proteinase K digestion of bacteria was carried out following the manufacturer’s protocol.

tag: strain

value: ATCC 8739


title: Evolved 2

description:
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Evolved_2


title: Evolved 1

description:
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Evolved_1


title: Condition 3-3

description:
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Con_3_3


title: PolII_UNT_4

tag: cell line

tag: cell type

value: Human osteosarcoma cell line

tag: treated with

value: mock

tag: chip antibody


title: CLIP-seq, IP, HA-Ago2 Replicate A

city: Cambridge

first: Amanda

last: Whipple

state: MA

address: 16 Divinity Ave

department: Molecular & Cellular Biology

institute: Harvard University

description: CLIP-seq

data_processing:
For small RNA-seq and CLIP-seq data, adapter sequences were trimmed using cutadapt (v1.4.2) or fastxtoolkit (v0.0.13).
For CLIP-seq data, reads were collapsed by unique molecular identifier (UMI) and then the UMI was trimmed using fastxtoolkit (v0.0.13).
STAR (v2.4.1d) was used to map sequencing reads to mm10 genome (Gencode M15 assembly) and transcriptome.
RSEM (v1.2.30) was used to count transcriptome mapped reads.
Quantification of RSEM counts was performed using DESeq2.
For CLIP-seq data, biological replicates were merged using samtools. Peaks were called on HA-Ago2 IP sample using CLIPper tool. Then, enrichment for Ago2 binding at each peak was calculated in HA-Ago2 IP samples relative to HA-Ago2 Input and untag-Ago2 IP using seCLIP perl scrips from the Yeo lab (https://github.com/YeoLab/eclip).
Genome_build: mm10
Supplementary_files_format_and_content: mapped reads (STAR output) as bam files, expression values (RSEM output) as tab-delimited text files, and differential gene expression (DESeq2 output) as tab-delimited text files.

source_name: induced neurons

growth_protocol: ESCs were grown in ESC medium containing 10% FBS + LIF. iNs were generated by doxycycline-induction of TetO-Ngn2 in neuron differentitiation medium for 10 days.

extract_protocol:
Cells were washed in 1X PBS and then UV crosslinked at 400 mJ/cm2. Immunoprecipitation was performed with anti-HA magnetic beads (Pierce) overnight at 4°C.
seCLIP-seq libraries were prepared according to (Van Nostrand et al., 2017) with TruSeq LT adapters. Input and IP samples were amplified with 9 and 18 cycles of PCR, respectively. Quality control on final libraries was assessed with a fragment analyzer and qPCR for colony forming units prior to pooling and loading on an Illumina FlowCell (HiSeq2000, 40 bp SE reads).

value: induced neurons

tag: differentiation day

value: Day 10

value: Replicate A

tag: genotype

value: Mirg(fl/+)

tag: expressing

tag: rip antibody

value: anti-HA


title: CLIP-seq, IP, HA-Ago2 Replicate B

description: CLIP-seq

value: Replicate B


title: CLIP-seq, IP, untag-Ago2 Replicate A

description: CLIP-seq


title: CLIP-seq, Input, HA-Ago2 Replicate B

description: CLIP-seq


title: CLIP-seq, Input, HA-Ago2 Replicate A

description: CLIP-seq


title: CLIP-seq, IP, untag-Ago2 Replicate B

description: CLIP-seq


title: hMSCs donor 1 chondrogenesis day 10

first: Rodrigo

middle: A

last: Somoza

state: Ohio

address: 2080 Adelbert Rd

description:
hMSCs donor 1 chondrogenesis day 10
1-d10

hyb_protocol: The cRNA was hybridized to Illumina BeadChips

scan_protocol: BeadStation array reader according to the manufacturer’s instructions (Illumina).

data_processing: Raw microarray data of the cell clones was normalized with the R beadarray library

source_name: Bone marrow

label_protocol: Total RNA was linearly amplified and biotin labeled using Illumina Total- Prep  kits (Life Technologies, CA)

growth_protocol: Cultures of hMSC from two healthy deidentified adult volunteer donors were established as previously described. The bone marrow was collected using a procedure reviewed and ap- proved by the University Hospitals of Cleveland Institutional Review Board; informed consent was obtained from all dei- dentified donors. Cells were expanded in Dulbecco’s modified Eagle’s medium-low glucose with fetal bovine serum 10% (selected batch) supplemented with 10 ng/mL fibroblast growth factor (FGF)2.

extract_protocol: Total RNA was prepared from tissues in RNAlater (Qia-gen) after the addition of TRIzol (Life Technologies) and homogenized with a Polytron (PT-MR2100; Polytron Corp.). Following the transfer ofprocessed sample to Qiagen RNeasy mini columns, the extraction of total RNA was performed according to the manufacturer’s instructions. For hBM-MSC- derived cartilage, aggregates were homogenized with RNase- free disposable Pellet-Pestles? (Kimble-Chase, TN), digested on-column with DNase-I, and purified with the RNeasy mini kit. RNA

treatment_protocol: hMSCs were cultured in cell aggregates (3D pellets) in complete chondrogenic medium (DMEM-high glucose supplemented with 1% ITS+,10-7 M dexamethasone, 1mM sodium pyruvate, 120mM ascorbic acid-2 phosphate, 100mM nonessential amino acids, and 10ng/mL TGF-b1). Chondrogenic pellets were harvested at different time points (3, 7, 10, 14, 21, and 28 days) for RNA extraction and microarray analysis. A day 0 sample was also included that corresponds to hMSCs in monolayer culture before chondrogenic induction.

value: chondrogenesis day 10

tag: gender

value: Female

tag: age


title: hMSCs donor 2 chondrogenesis day 3

description:
hMSCs donor 2 chondrogenesis day 3
2-d3

tag: time point

value: chondrogenesis day 3


title: hMSCs donor 2 chondrogenesis day 14

description:
hMSCs donor 2 chondrogenesis day 14
2-d14

value: chondrogenesis day 14


title: hMSCs donor 1 chondrogenesis day 14

description:
hMSCs donor 1 chondrogenesis day 14
1-d14


title: hMSCs donor 2 chondrogenesis day 10

description:
hMSCs donor 2 chondrogenesis day 10
2-d10


title: HBL1 CsA 24h r3


title: hMSCs donor 1 chondrogenesis day 28

description:
hMSCs donor 1 chondrogenesis day 28
1-d28

value: chondrogenesis day 28


title: Human neonatal articular cartilage donor 1 [hNAC-2]

description:
Human neonatal articular cartilage donor 1
hNAC-2

source_name: Knee cartilage

value: Male


title: hMSCs donor 2 chondrogenesis day 7

description:
hMSCs donor 2 chondrogenesis day 7
2-d7

value: chondrogenesis day 7


title: hMSCs donor 1 chondrogenesis day 21

description:
hMSCs donor 1 chondrogenesis day 21
1-d21

value: chondrogenesis day 21


title: hMSCs donor 2 chondrogenesis day 21

description:
hMSCs donor 2 chondrogenesis day 21
2-d21


title: Human neonatal articular cartilage donor 1 [hNAC-1]

description:
Human neonatal articular cartilage donor 1
hNAC-1


title: hMSCs donor 1 chondrogenesis day 3

description:
hMSCs donor 1 chondrogenesis day 3
1-d3


title: hMSCs donor 2

description:
hMSCs donor 2
2-d0


title: hMSCs donor 1 chondrogenesis day 7

description:
hMSCs donor 1 chondrogenesis day 7
1-d7


title: CLIP-seq, Input, untag-Ago2 Replicate B

description: CLIP-seq


title: Condition 3-1

description:
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Con_3_1

value: ATCC 8739


title: hMSCs donor 2 chondrogenesis day 28

description:
hMSCs donor 2 chondrogenesis day 28
2-d28


title: Condition 11-3

description:
Reference
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Con_11_3


title: CLIP-seq, Input, untag-Ago2 Replicate A

description: CLIP-seq


title: hMSCs donor 1

description:
hMSCs donor 1
1-d0


title: Condition 11-2

description:
Reference
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Con_11_2


title: Condition 11-1

description:
Reference
processed data file: Supplementary_file_S1.xlsx
Supplementary_file_S1.xlsx: Column Con_11_1


title: shSASH1-rep2

city: Dalian

first: dapeng

last: Liang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

data_processing:
Clean reads were retained by removing reads containing adapter, reads containing ploy-N and low quality reads using in-house perl scripts
Clean reads were aligned to the hg38 genome assembly using STAR
STAR with --quantMode option was used to generate gene-level count matrix as input for DESeq2 statistical model
Convert Ensembl IDs to Entrez IDs and discard any unmapped features. Multimapped Ensembl IDs were also discarded to enforce unique mapping. Only features with unique Ensembl ID to Entrez ID mappings were retained.
Differential expression analysis between shSASH1 and shControl cells was performed using DESeq2 package
Genome_build: hg38
Supplementary_files_format_and_content: csv file include TPM expression value and gene annotation

source_name: MDA-MB-468 cells

growth_protocol: MDA-MBA-468 cells were routinely generated by re-plating with DMEM supplied with 5% FBS.

extract_protocol:
RNA was isolated from MDA-MBA-468-shSASH1 or MDA-MBA-468-shControl cells using TRIzol Reagent.
The sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions.

treatment_protocol: Cells were infected with pGIPZ-CTRL and SASH1-shRNA lentiviruses, and stable clones were selected using puromycin.

value: breast cancer epithelial cells

tag: tissue

value: breast

tag: knockdown


title: Small RNA-seq, Mirg(Delta/+) iN Replicate C

description: Small RNA-seq

extract_protocol:
Total RNA was extracted using TRIzol. Small RNA-seq libraries were prepared using QIAseq miRNA Library Kit (Qiagen).
Small RNA-seq libraries were prepared from 100 ng DNase-treated RNA using QIAseq miRNA library kit (Qiagen) with 16 cycles of PCR amplification. Quality control of final libraries was assessed with a fragment analyzer and qPCR for colony forming units prior to pooling and loading on an Illumina FlowCell (HiSeq2000, 40 bp SE reads).

value: induced neurons

value: Replicate C

value: Mirg(Delta/+)


title: Small RNA-seq, Mirg(fl/+) iN Replicate C

description: Small RNA-seq

value: Day 10

value: Mirg(fl/+)


title: Small RNA-seq, Mirg(Delta/+) iN Replicate A

description: Small RNA-seq

value: Replicate A


title: shSASH1-rep1


title: Small RNA-seq, Mirg(Delta/+) iN Replicate B

description: Small RNA-seq

value: Replicate B


title: Small RNA-seq, Mirg(fl/+) iN Replicate B

description: Small RNA-seq


title: shControl-rep1

value: control


title: Small RNA-seq, Mirg(Delta/+) ESC Replicate C

description: Small RNA-seq

source_name: Embryonic stem cells

value: Embryonic stem cells

value: Day 0


title: Small RNA-seq, Mirg(Delta/+) ESC Replicate B

description: Small RNA-seq


title: Small RNA-seq, Mirg(fl/+) iN Replicate A

description: Small RNA-seq


title: shControl-rep2


title: RNA-seq, Mirg(Delta/+) iN Replicate A

description: rRNA-depleted RNA-seq

extract_protocol:
Total RNA was extracted using TRIzol. rRNA-depleted RNA-seq libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems).
rRNA-depleted RNA-sequencing libraries were prepared from 400 ng DNase-treated RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) using 9 cycles of PCR amplification. Quality control on final libraries was assessed with a fragment analyzer and qPCR for colony forming units prior to pooling and loading on an Illumina FlowCell (NextSeq 500, 75 bp PE reads).


title: RNA-seq, Mirg(Delta/+) iN Replicate B

description: rRNA-depleted RNA-seq


title: Small RNA-seq, Mirg(fl/+) ESC Replicate B

description: Small RNA-seq


title: RNA-seq, Mirg(fl/+) iN Replicate C

description: rRNA-depleted RNA-seq


title: RNA-seq, Mirg(Delta/+) iN Replicate C

description: rRNA-depleted RNA-seq


title: Small RNA-seq, Mirg(fl/+) ESC Replicate C

description: Small RNA-seq


title: Small RNA-seq, Mirg(fl/+) ESC Replicate A

description: Small RNA-seq


title: RNA-seq, Mirg(fl/+) iN Replicate B

description: rRNA-depleted RNA-seq


title: RNA-seq, Mirg(fl/+) iN Replicate A

description: rRNA-depleted RNA-seq


title: sorted_Hardy_fraction_BC_Ikaros_ZnF4-/-

city: San Francisco

first: Hilde

last: Schjerven

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

description:
dF4-BC
polyA mRNA enriched from Total RNA

data_processing:
Raw data (fastq) was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Giardine et al., 2005; Trapnell et al., 2009; Blankenberg et al., 2010a; Blankenberg et al., 2010b; Fujita et al., 2010; Goecks et al., 2010).
Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Relative mRNA expression levels (RPKM) (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
Filtering and calculation of Relative changes in expression levels between samples were analyzed in excel.
Genome_build: mm9 [the July 2007 annotation of mouse (Mus musculus) genome data]
Supplementary_files_format_and_content: Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Supplementary_files_format_and_content: Attached as supplemental file on the Series record are the unfiltered RPKM values for all annotated Refseq genes (as a Tab delimited .txt file)

source_name: sorted proB cells from primary Bone Marrow (BM)

growth_protocol: none - primary cells

extract_protocol: Illumina TruSeq

treatment_protocol: Single cell suspensions were prepared from sorted proB cells from mouse bone marrow (age of mice: 6-7 weeks).

tag: genotype/variation

value: bone marrow (BM)

value: sorted primary proB cells

tag: developmental stage

value: Hardy fraction B+C+C'


title: RNA-seq, Mirg(Delta/+) ESC Replicate B

description: rRNA-depleted RNA-seq

tag: replicate


title: RNA-seq, Mirg(Delta/+) ESC Replicate A

description: rRNA-depleted RNA-seq


title: sorted_Hardy_fraction_BC_wt

description:
wt-BC
polyA mRNA enriched from Total RNA

tag: strain

value: wild type


title: sorted_Hardy_fraction_BC_Ikaros_ZnF1-/-

description:
dF1-BC
polyA mRNA enriched from Total RNA


title: RNA-seq, Mirg(fl/+) ESC Replicate C

description: rRNA-depleted RNA-seq


title: Small RNA-seq, Mirg(Delta/+) ESC Replicate A

description: Small RNA-seq


title: P6_10

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

institute: Helmholtz Zentrum München

description: scRNA-seq

data_processing:
Raw sequencing data for both single cell and bulk experiments were controlled for quality and trimmed.
For scRNA-seq paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Bulk RNA-seq data were mapped to the reference mm10 genome using STAR (Dobin et al., 2013).
The identity of reads was identified through FeatureCount (Liao et al., 2014).
For scRNA-seq analyses, the RNA expression matrices from each cell were merged and further analysed with RaceID3 software package (Herman et al., 2018).
For both scRNA-seq and the bulk Brain-FACS RNA-seq analyses, differentially expressed genes between the cell types or cell clusters were identified using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited and csv text files include count matrices for scRNA-seq data and bulk RNA-seq samples

source_name: E14.5 brain

extract_protocol:
Mouse E14.5 brain was dissociated and either mCEL-Seq2 protocol for scRNA-seq or population-based FACS-sorting and bulk RNA-seq was performed.
scRNA-seq libraries were prepared according to mCEL-Seq2 protocol. Libraries were sequenced on an Illumina HiSeq 3000 sequencing system (pair-end multiplexing run, high output mode) at a depth of ~200,000 reads per cell. Population-based FACS-sorting and bulk RNA-seq  from neural cells was isolated using the Qiagen mini kit (#74104), while RNA from mural cells, endothelial cells and microglia was extracted using the Qiagen miRNeasy Micro kit (#1071023). Libraries for RNA-seq of the neural population were prepared using the Illumina TruSeq library preparation kit. For mural cells, endothelial cells and microglia, cDNA was prepared from isolated RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech 634891). Libraries were prepared using the Nextera XT DNA library preparation kit (Illumina FC-131-1096) and sequenced on the HiSeq 2500 instrument.
scRNA-seq

value: Mof Knockout


title: P6_11

description: scRNA-seq


title: RNA-seq, Mirg(fl/+) ESC Replicate B

description: rRNA-depleted RNA-seq


title: P6_12

description: scRNA-seq